Quasi-Hamiltonian equations of motion for internal coordinate molecular dynamics of polymers

Conventional molecular dynamics simulations macromolecules require long computational times because the most interesting motions are very slow compared with the fast oscillations of bond lengths and bond angles that limit the integration time step. Simulation of dynamics in the space of internal coordinates, that is with bond lengths, bond angles and torsions as independent variables, gives a theoretical possibility to eliminate all uninteresting fast degrees of freedom from the system. This paper presents a new method for internal coordinate molecular dynamics simulations of macromolecules. Equations of motion are derived which are applicable to branched chain molecules with any number of internal degrees of freedom. Equations use the canonical variables and they are much simpler than existing analogs. In the numerical tests the internal coordinate dynamics are compared with the traditional Cartesian coordinate molecular dynamics in simulations a 56 residue globular protein. For the first time it has been possible to compare the two alternative methods on identical molecular models in conventional quality tests. It is shown that the traditional and internal coordinate dynamics require the same time step size for the same accuracy and that in the standard geometry approximation of aminoacids, that is with fixed bond lengths, bond angles and rigid aromatic groups, the characteristic step size is 4 fsec, that is two times higher than with fixed bond lengths only. The step size can be increased up to 11 fsec when rotation of hydrogen atoms is suppressed.